[phenixbb] Autobuild error message

Tom Terwilliger terwilliger at lanl.gov
Fri Aug 13 12:03:59 PDT 2010

Hi Bryan,
I'm sorry for the trouble!

AutoBuild is running phenix.refine and asking it to write out  
"refine_pdb_in.mtz".  After phenix.refine is done, it looks for this  
file and if it is missing it will stop.

There are two possibilities. Can you check if the file is really  
missing or not:

ls -ltr AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz

1. AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz really is missing:  This  
means that something has gone wrong that is not anticipated. Can you  
in this case send me the data to run here?  If not, have a look at the  
last set of files written in AutoBuild_run_2_/TEMP0/ ... do these log  
files help in any way?

2.  AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is not missing, it was  
just written after the check for its presence was over.  This can  
happen if you are on an nfs file system and it is slow.  I have just  
finished adding code to AutoBuild to wait for files to appear to get  
around this problem...so if you try tomorrow's build it is possible  
this will be fixed. You may need to change the parameter  
"max_wait_time" to a longer time (default=0.1 sec).

Let me know if this doesn't do it!
All the best,
Tom T

On Aug 13, 2010, at 12:46 PM, <bschmidt at berkeley.edu> wrote:

> Hello all,
> I am trying to use phenix.autobuild from the command line to  
> generate either composite omit maps or prime and switch maps. In  
> either case, when I try, the program starts to run for a while  
> before failing and giving me the following error message:
> "Failed to carry out AutoBuild_build_cycle:
> Sorry...the file AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is  
> missing..."
> I'm not sure why that would be the case, or where that mtz is  
> supposed to come from. Can anyone explain what might be the problem?
> Thanks,
> Bryan
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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